Viruses

Define virus

Non-cellular agents that infect cells and reproduce using the genetic material in the host cell. Non-living, non-cellular parasite. Consists of nucleic acid surrounded by a protein coat (capsid).

What is the most likely cause of a period of lysogeny?

A repressor protein coded by viral DNA, prevents transcription and translation of viral protein. This allows the virus to remain dormant within the host cell.

What viral feature correlates to the size of the genome?

Size and shape of the capsid because it must be large enough to enclose the viral genome.

Explain how viruses infect prokaryotic cells and how this process differs from viral infection of eukaryotic cells.

Eukaryotic cells

• Viral infection ivolves endocytosis

• Virus enters cell in membrane-bound vesicle

• Virus envelop fuses with vesicle membrane to release its genome

• Eukaryotic viruses can integrate into host genome for persistent infections (remains in the host and can reactive later to produce new viral particles)

Prokaryotic cells (for bacteriophage)

• Attatchment to specific repcotrs on bacterial cell wall

• Direct injection of viral DNA/RNA through cell wall

• Viral genetic matieral uses host cell machinery for replication

• Cell lysis releases new viral particles

Explain how the envelope helps viruses evade the host immune system and enhance their infectivity.

Enveloped proteins cotians host cell phospholipds (plama membrane) virally-encoded in its glycoprotein spikes outside the envelope through the fusing between viral and hsot cell membranes. (Coranavirus takes the internal membrane instead). The viral envelope protects the virion (the isolated virus particle outside the host cell) from enzymes and other chemicals, giving them an advantage over virions with only a capsid.

The glycoproteins also helps viruses enter host cells by binding to receptor molecules on the cell surface. Virions recognize and bind to specific host proteins, resulting in many virions entering the host cell.

What are the differences between antigenic drift and antigenic shift?

Antigenic drift:

• Small incremental changes over viral genetic material over time

• Slowly produces varaition of the surface proteins in virus

• Accumulated changes can eventually prevent immune system from recognzing virus

• Example: HIV virus undergoes very rapid antigenic driftm, even in single individual

Antigentic shift:

• Two or more different viral strains (genetic variant of virus) or different viruses infect same cell and recombine genetic material.

• Produces major changes to surface protein of virus in short time

• Creates new virus that is capable of creating pandemics because immune system can not recgonize new strain

• Example: Influenzavirus can undergo antigentic shifts to create “new” viruses. Vaccines must be regulary updated

Compare and contrast lytic and lysogenic life cycles in viruses

Compare:

• Viral entry into host cell

• Releases viral genetic information into host cell
  

Contrasts:

• Lytic cycle is immediate/rapid viral replication after infection

• Lytic cycle causes death of host cell through lysis/bursting of cell

• Lysogenic cycle: Viral replication occurs along with host cell division because its DNA becomes incorporated into host cell’s genome

• Lysogenic cycle eventually switches to lytic cycle after viral DNA is seperated/excised from host cell’s genome during stressful conditions.

Describe the 3 different hypothesis of the origin of viruses

Virus first hypothesis: Viruses orignated before cells and evolved. Came from bits of RNA with self-complementary sequences (fold itself like a protein). Gradually it became more complex and could self-replicate and began infection other cells.

Regressive/reduction/degeneracy hypothesis: Virus were once of small cells that became parasites of larger cells.

Escape gene/vagrancy hypothesis: Virus came from portions of genetic material (DNA/RNA) escaped from larger organisms like bacteria and slowly became surrounded by outer boundry.

Discuss the strategies used to control viral outbreaks.

• Vaccination programs to prevent viral transmission and build immunity

• Quarantine/isolation measures for infected individuals

• Public health campaigns to promote personal hygiene, social distancing, proper use of protective equipment like masks/face guard

• Travel restrictions and border control to limit viral spread

• Development and distribution of antiviral treatments

Define covergent evolution and its relation to the origin of viruses

Process that occurs when species occupy similar ecological niches and adapt in similar ways in response to selective pressures. Traits that arise through convergent evolution are called analogous structures.

Evidence to support this is that all viruses have same features despite their diversity:

• Genetic material (RNA/DNA)

• Capsid and no cytoplasm

• None can carry out life functions

Explain how reverse transcriptase allows retroviruses to replicate within a host cell.

Reverse transcriptase is an ezyme carried by retroviruses which converts/transcribes viral RNA into DNA. The process occurs after the virus enters a host cell and integrates into the host’s genome, allowing viral genes to be transcribed by host cell machinery. New viral proteins and RNA genome are produced using host cell resources. Virus replicates when host cell divides/reproduces.

Define a bacteriophage lambda

(Phages for short)
Viruses that infect bacteria. Key role in development in molecular biology. Provides a way to show how genes are transferred from one bacterium to another. Very specific in the bacteria they infect.

Bacteriophage lambda infects only E.coli. Can enter through lysogenic or lytic cycle which kills bacterial cell.

Give examples of enveloped and non-enveloped viruses

Enveloped: HIV, influenza virus, coranavirus

Non-enveloped: Bacteriophages/poliovirus

Define a virion

an isolated but infectious virus particle found outside the host cell. Viral envelope protects the virion from enzymes and other chemicals, giving them an advantage over virions with only a capsid.

Outline the characterisitcs of bacteriophage lambda

• linear DNA

• complex capsid with an icosahedral head, tail sheath, and one tail fibre

• naked virus (no envelope)

• host cell = bacteria E. coli

• lytic and lysogenic cylces

• tail fiibre attatches to receptor of surface of host cell

• non-contractile tail sheat inserts viral genome into host cell. Capsid is oustide of host cell

• integrated into bacterial host chromosomes as prophage in the lysogenic cycle

• DNA of host cell is degraded during lytic stage

• transcription and translation done by host cell machinery

• when lytic cycle induced = prophage reomved from bacterial host chromosome where osmotic lysis occurs that kills host cell and releases phage particles

Define a lytic life cycle

Lytic cycle is a phage life cycle where a phage attracts to a host bacterium, injecting its DNA to undergo replication to form new virions (viruses) which lyses (breakdowns) the host cell. Bacteriophages that only use lytic cycles are called virulent phages

Define coronavirus

Large and diverse family of RNA viruses that cause respiratory diseases in animals and humans. They were prior to the 2019 pandemic, first found in the 1960s. SARS-CoV-2 is the virus that caused the COVID-19 disease which was thought to be transferred from an animal host to humans in late 2019.

Define SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2, the virus that causes COVID-19.

Define a lysogenic life cycle

phage life cycle where a phage attaches to a bacterium and injects its genome, but it does not undergo a full replication cycle. It becomes in a state of dormancy where it gets replicated along host cell’s DNA during cell division to spread virus’s genetic material.

Define parasite

Organism that lives on/in another organism (host) for majority of its life cycle.

Define bacteria

Tiny, unicellular, living organisms that is found nearly everywhere

Define capsid

Protein coat of virus that protects DNA. Made of capsomere (protein subunits)

Define microorganism

Living organism that cannot be seen by the naked eye, including bacteria, viruses, fungi, and protozoa.

Differentiate between pandemic, epidemic, and outbreak

Pandemic- Epidemic that spreads globally
Epidemic- Widespread outbreak of disease in region
Outbreak- Sudden increase in number of cases of disease in specific area

State the differences in structure between a bacterial cell and a virus

Bacteria:
Cellular

Small diameter (1-5 µm)

Both DNA and RNA

70S ribosomes

Some move by rotating flagella

Binary fission

Virus:

Non-cellular

Extremley small diameter (0.02-0.2 µm)

Either DNA or RNA (never both)

Ribosomes are rarely present

No movement (can not move on thier own, must move through host cell)

Viral replication (protein sythesis, self-assembly, inside host cell)

Outside surface is protein capsid and lipoprotein envelope (for some)

What are the features of every virus?

Extremely small (20-300 nm) thus needs electron microscope
Nucleic acid as genetic material (DNA or RNA). Not enclosed in nucleus membrane
Few/no enzymes
No cytoplasm
Capsid made of protein surrounds the nucleic acid

State the reasons of the diversity of structure in viruses

Different genetic materials

• DNA viruses

• RNA viruses

Different Envelopes

• Enveloped

• Non-enveloped

Different Virus Structure

• Sphereical (influenza/COVID)

• Complex (bacteriophage)

• Helical (tobacco mosaic virus)

• Polyhedral (adenovirus)

Different Capsid Structure

• Helical, icosahderal, complex structure
  

Evolutionary factors

• Mutation

• Recombination

• Reassortment

• Selection

Different ways of mutation

• Antigentic drift (gradual)

• Antigentic shift (rapid)

Outline the structure of a HIV virus

• spherical shape

• Glycoprotein spikes (made of protein and carbhydrate. It is how it attatches to host cell aka CD4 white blood cells in humans)

• Capsid

• Viral envelope

• 2 identical RNA strands (not combined)

• Reverse transcriptase (production of DNA using viral RNA as a model)

Outline the structure of a coranavirus

• Spherical shape

• single stranded RNA

• envelope outside of capsid

• numerous projections of spike proteins (corona or crown) that latches on specific receptors on host cells. Different types of host cells are affected by different viruses. For coronaviruses it binds to respiratory tracts and envelope merges with the host’s cell membrane

Outline the feature of bacteriophage lambda

• Capsid head that protects double-stranded DNA core

• Tail fibres that attatch to virus of host cell

• Tail sheath that consists of proteins that contract to puncture tail tube thorugh host cell’s outer membrane

• DNA is injected through tail, into the host cell

Define positive sense strand virus

Viral RNA that has the same base sequence as mRNA. RNA is from 5’ to 3’ direction. Can be directly translated into proteins by host cell.

Define negative sense strand virus

Viral RNA that is complimentary to mRNA (antisense strand) so it cannot directly encode for protein synthesis. Must be replicated to mRNA before protein production can begin. RNA is from 3’ to 5’ direction. Can not be directly translated into proteins by host cell. Must be transcribed into 5’ to 3’ direction RNA (positive sense) by an RNA polymerase before translation can occur.

Enveloped virus vs Non-enveloped virus

Enveloped- Has lipid bilayer envelope surrounding protein capsid.
Less stable on surfaces and more susceptible to environmental factors and disinfectants.
Envelope is very fragile/sensitive.
Dry surfaces can kill envelope viruses

Glycoproteins on envelope surface binds to specific host cell receptors

Contains host proteins (since envelope is derived from host cell’s membrane) that help virus appear less foreign to immune system

Envelope derived from host cell membrane

Non-enveloped-
Lacks external membrane.
More resistant to temperature, pH, dryness, and simple disinfectants.
The protein capsid is stronger.

Outline the stages of the lytic cycle

1. Attatchment: Phage attaches to surface of host cell

2. Penetration: Phage penetrates the host cell and releases its viral DNA into host cell

3. Biosynthesis: Phage DNA replicates and bacterial DNA is broken down (DNA hydrolysis takes place)

4. Maturation: Phage protein synthesis using ribosomes of host cell. Assembly of new phage virus

5. Release: Cell lysis (breakdown of host cell) as the newly made phagge particles are released

6. Spread and reproduce (repeat steps)

Outline the stages of the lysogenic cycle

1. Phage infects cell

2. Phage DNA becomes incorporated into host genome. Inserting viral DNA to alter genotype of bacterium/host cell

3. Cell divides. Bacterial chromoosmes is copied and phage’s DNA is replicated and passed to daughter cells in reproduction

4. Under stressful conditions, phage DNA is removed from bacterial chromosome and enters lytic cycle

5. Phage DNA replicates and phage proteins are made. New phage particles areassembled

6. Cell lyses, releasing phages

How can virus move?

Not independently. They move passively through phloem, blood, other body fluids, or the air. If it

Define the progressive/escape hypothesis

Explanation for the evolution of virus. It suggests that viruses evolved from genetic elements (DNA, RNA) that escaped from host cells (bacteria) and became a virus.

Define the regressive(reduction/degeneracy) hypothesis

Virus came from some host cells and over time it lost its cellular organelles and became reduced to a parasite of larger cells.

Define the virus first hypothesis

Viruses originated before cells because of its simplicity and over the course of evolution became more complex. It suggest that ancestors of modern viruses could provided the materials necessary for the development of the first cells.

What are some reasons for the rapid rates of evolution of viruses

The average generation time is less than an hour compared to human’s 25 years. Mutation rates are also extremely high in viruses due to its lack of proofreading during virus genomoe replication.

What are the differences between a variant and a new chain

Variant- Change in RNA from original parental strain/virus
New strain- Change in RNA and virus behavior from original parental strain/virus

How is the high mutation rate favor viruses

Natural selection favors diverse variations making virus more likely to live and rapidly multiply.

Define influenza virus

Negative sense virus
RNA replicase
No DNA polymerase (no proofread so high rate of mutation)
Has 8 separate RNA molecules = new strain of virus can appear
Easily killed

Function of integrase proteins

Integrates viral DNA into host cell’s genome.

Outline the methods of HIV transmission and its effects on the immune system

The glycoproteins outside the HIV’s envelope binds to the host cell, which is the CD4 white blood cell in humans. HIV can get transmitted by unprotected sexual intercourse, sharing needles, or breast feeding. It destroys the infection-fighting CD4 cells or helper T cells, making it difficult for the body to fight off infections, illnesses, and certain cancers. Without correct treatment, the HIV infection can progress into AIDS, resulting in the immune system becoming severely compromised.

Why is international cooperation needed to fight contagious diseases?

• Contagious disease can cross borders which can cause pandemic

• Medicine knowledge must be shared

• Mass vaccination programs are needed to prevent spread of disease

• Developed countries can give financial and medical support for developing countries

• Share knowledge and expertise

Antibiotics are an essential tool of modern medicine. Outline the strengths and limitations of antibiotics

Strengths

• Able to prevent more widespread of diseases by killing viruses

• Antibiotics do not harm eukaryotic/body cells

• Antibiotics are fast acting (instant relief)

Limitations

• Due to the high mutation rate of viruses, it is difficult to have a truly effective antibiotic to kill of viruses.

• Viruses can create new viral strains rapidly (eg. influenza virus), resulting in antibiotics to be regularly updated

• Antibiotics can have side effects or cause allergic reactions

• Misuse of antibiotics can lead to increased antibiotic resistance of viruses

• Limited number of antibiotics available to fight bacterial infections due to high costs and time to develop them

Discuss the role of viruses in gene transfer, using examples such as bacteriophages in transduction and retroviruses in horizontal gene transfer:

Bacteriophages in transduction:

• Infect bacterial cells

• Incorporate host bacterial DNA into viral geome

• Transfer DNA to new bacteiral host during next infection

• Results in genetic variation in bacteria

Retroviruses in horizontal gene transfer:

• Contains RNA genome

• Reverse transcription to convert RNA to DNA

• Integration of viral DNA into host genome

• Transfer viral genes to host organism